Fall 2013 Schedule


Date Speaker
8/29 Tung Le (Kim Lab)
9/12 Ilija Uzelac (Fenton Lab)
9/19 Keith Carroll (Curtis Lab)
9/26 Henry Astley (Goldman & Hu Lab)
10/3 Mark Kingsbury (Goldman Lab)
10/10 Curtis Malusek (Gumbart Lab)
10/17 Fall Break
10/24 Gable Wadsworth (Kim Lab)
10/31 Luis Jover (Weitz Lab)
11/7 Guillermo Amador (Hu Lab)
11/14 Jeff Aguilar (Goldman Lab)
11/21 Karl Lundquist (Curtis Lab)
11/28 Thanksgiving Break
12/5 Patricia Yang (Hu Lab)

Link to editable google doc here.

Fall 2013 Abstracts



Karl Lundquist, Curtis Lab

The pericellular matrix (PCM) is a large polymer mesh which is grafted to the surface of many Eukaryotic cells. This coat is composed primarily of a Hyaluronan backbone and proteoglycans such as aggrecan and versican. Studies have shown that the PCM plays a critical role in various cellular processes including migration, mechanotransduction, molecular sequestration, and virtually every other cell process which requires communication between the outside and inside of the cell. However, due to the extremely high water content in the coat, the PCM cannot be visualized using traditional imaging methods. Considering this, and the contribution of the PCM to countless cellular processes, it is empirical to develop novel assays for probing the properties of the matrix. Work in our laboratory has generated such assays but has yet to apply them to characterize the differences in cellular coats that exist between distinct cell types and during physiological transformations like migration and mitosis. I will discuss future work addressing the role that the PCM plays in cellular processes, as well as provide a summary of results obtained in the Curtis lab.



Jeff Aguilar, Goldman’s Lab

Various animals exhibit locomotive behaviors involving fast impulsive interactions with granular media, such as sprinting, jumping and hopping. On hard ground, these behaviors can be piece-wise described as transient bursts of actuation coupled with internal elastic elements to generate movement. On granular media, however, the performance of these behaviors is subject to the reaction forces of the media upon foot intrusion. The laws that govern these forces are not fully understood and vary with size and shape of foot, volume fraction and speed of intrusion. To better understand these interactions, we study the performance of vertical jumping on granular media of an actuated spring mass robot. The robot performs single jumps via one-cycle sine-wave relative trajectory. We systematically vary the forcing frequency and volume fraction and find that, at 8 Hz forcing, there is 743% increase in jump height with only a 5% increase in volume fraction using a 2” diameter flat foot. Additionally, including a short, high speed downward push prior to the main sine-wave movement nearly doubles the jump height at high volume fractions.



Guillermo Amador, Hu’s Lab

Flying insects face a barrage of foreign particles such as dust and pollen, which threaten to coat their eyes and antennae, limiting their sensing abilities. In this study, we elucidate novel aerodynamic and elastic mechanisms by which insects keep these organs clean. The compound eye of many species of insects is covered by an array of short bristles, or setae, evenly spaced between photoreceptor units. Among these insect species, setae length is roughly equal to their spacing. We conduct numerical simulations and wind tunnel experiments using an insect eye mimic to show setae of this length reduce shear rate at the eye surface by up to 90%. Thus, the setae create a stagnant zone in front of the eye, which diverts airflow to reduce deposition of particles. Setae can also act as springboards to catapult accumulated particles. In high speed videography of insects using their legs to clean themselves, we observe deflected setae and antennae hurling micron scale particles at accelerations 100-1000 times earth’s gravity. The dual abilities of setae to divert airflow and catapult particles may motivate bio-inspired designs for dust-controlling lenses, sensors, and solar panels.



Luis Jover, Weitz’s Lab

Viral lysis of host cells in marine environments leads to the release of cellular carbon and nutrients and is hypothesized to be a major driver of carbon recycling at global scales. However, prior efforts to characterize the effect of viruses on carbon recycling have focused on materials in the host and overlooked the geochemical potential of viral particles themselves, particularly with respect to their nitrogen (N) and phosphorus (P) content. In this Analysis article, we propose a biophysical scaling model of the elemental stoichiometry of intact bacteriophage particles, finding that bacteriophage differ strongly in terms of their elemental stoichiometry from that of their host microorganisms. In conjunction with comparisons to the genomic and proteomic content of known virus isolates, we extrapolate this particle-scale model to ecosystem scales and predict that, despite their typically sub-femtogram total mass, bacteriophage particles – and virus particles more generally – are stronger contributors than previously recognized to both the reservoir and recycling of marine organic N and P.



Gable Wadsworth, Kim’s Lab

Gene expression is an ongoing process in all living organisms. Genetically identical cells can exhibit different gene expression patterns. Understanding the origin of this diversification is one of the main research goals in biology. To study how structure and dynamics of the physical genome affects stochastic gene expression, we have to measure either transcriptional dynamics of a single cell over time, or transcriptional statistics of a cell population at a fixed time from different genomic architectures. By implementing changes in the genetic code of the Pho5 promoter and open reading frame, gene expression can be quantified by measuring the amount of mRNA expressed by the cell. I will explain a technique called Fluorescence in Situ Hybridization (FISH), which is used to measure the number of mRNA in single cells. I will present improvements we made to this technique to achieve a true single-probe, single-fluorophore sensitivity in the model organism Saccharomyces Cerevisiae. Our technique allows the quantification of mRNA with a 1:1 ratio between mRNA molecule and FISH probe. To obtain this, mRNA spots are characterized in order to perform deconvolution and obtain super resolution images.



Mark Kingsbury, Stephen Gatesy, Daniel I. Goldman, Brown, Georgia Tech

In the mid 1800s, Edward Hitchcock founded the field of ichnology, or the branch of paleontology that studies traces of organismal behavior through burrows and footprints in substrates like mud and sand that flowed hundreds of millions of years ago. Initially, well preserved tracks of extinct animals like dinosaurs were measured with a ruler and protractor to help identify species and morphological characteristics of the organisms’ feet. Modern investigations study the intrusion of foot-shaped objects into laboratory mud (mimicking ancient beds) and observations of the footprints of living avian dinosaurs (like Guinea fowl) in prepared trackways. However, forced intrusions cannot capture how tracks emerge from the dynamical interactions of foot shape, ground properties and locomotion mechanics. And live organism studies suffer from controllability and repeatability. To systematically study how features of footprint formation are related to mass, gait, foot shape and size and substrate properties, we have built a self-supporting bipedal robot (39cm tall, 1.6 kg) that walks over prepared ground. We use an air fluidized bed of poppy seeds as our model substrate. Each leg is composed of four motors connected by segments which mimic avian limb morphology. The feet are 3D printed into different fixed shapes; we also test the effects of toe compliance. The robot is constrained by nearly frictionless horizontal and vertical air bearings; this structure allows translation but not pitching and avoids the need for feedback control to maintain the robot upright. The limbs and feet can be controlled to step in a specified trajectory. The entire system is under computer control, and we can systematically vary parameters, recording several hundred experiments per day. We present some preliminary data from our apparatus.



Henry C. Astley, Goldman’s Lab

Locomotion is an essential component of animal life history, and is strongly linked to morphology and physiology. Frog locomotion represents an ideal system in which to study locomotor performance, mechanics, and evolution. The exceptional jumping performance of anurans exceeds the capability of muscle due to a “catapult mechanism” in which an elastic element is slowly loaded by muscle, then rapidly recoils. Furthermore, anuran species employ a wide diversity of locomotor modes, with numerous independent evolutionary convergences and divergences. In this dissertation, I examined the performance and jump mechanics of a model taxon, followed by examining the evolution of muscle properties across the anuran phylogeny. Using X-ray Reconstruction of Moving Morphology (XROMM), I tested a candidate muscle-tendon unit for elastic energy storage by comparing muscle fascicle length change and ankle extension. These results showed that the muscle shortened early in the jump, stretching the elastic tendon, followed by rapid ankle extension without corresponding muscle shortening, indicating elastic recoil. However, prior laboratory performance measurements for this species (Rana pipiens) and congenerics suggested that no catapult mechanism was needed. To test this, I quantified jump distance of over 3000 bullfrog jumps at the Calaveras County Jumping Frog Jubilee. The majority of the jumps (58%) exceeded the maximum recorded in the scientific literature, in one case by almost a meter (2.2 m total), requiring the use of a catapult mechanism. To determine how this catapult mechanism was loaded prior to recoil, I used XROMM and force-plate data to compute inverse dynamics of frog jumping. Early in the jump, the hip moment and poor mechanical advantage impede joint motion, allowing the tendon to be loaded, after which hip moment declines and mechanical advantage improves, allowing tendon recoil. Examination of anatomical, performance, and muscle contractile property data across the frog phylogeny revealed that the evolution of performance was strongly linked to changes in anatomy, but minimally linked to changes in muscle properties. These result show that anurans do employ catapult mechanisms to produce high jump performance, using loading mechanisms widespread among vertebrates, and that the evolution of muscle properties is decoupled from locomotor performance.


Controlled Nano-scale Reactions with Thermochemical Nanolithography

Keith Carroll, Curtis Lab

ThermoChemical NanoLithography (TCNL) is a lithographic technique based on an Atomic Force Microscope (AFM) modified with a semi-conducting thermal cantilever. When brought into contact with a surface and heated, thermal cantilevers induce a narrow temperature profile and with a well-designed substrate, this localized heating can cause a chemical or physical transformation. While previous works focused primarily on different materials, there is limited research on controlling and understanding the underlying mechanisms governing the technique. In this talk, we show that by coupling the technique with a chemical kinetics model, surface reactions can be controlled down to the nano-scale. Having demonstrated excellent control, applications for biophysics are discussed.



Ilija Uzelac, Fenton’s Lab

Disruption of the normal heart rhythm can lead to a chaotic cardiac dynamic driven by the multiple scroll waves. If ventricular fibrillation (VF) develops, the cardiac intrinsic control system is unable to terminate it, and without any external control, death is imminent. In a phase space, the cardiac dynamic during normal heart rhythm is represented as a set of overlapping closed orbits that are destabilized during cardiac arrhythmias, mostly notably during VF. From the perspective of chaos theory and control theory of chaotic dynamics, parallels can be made with cardiac chaotic behavior and control methods can be devised. Time-delayed feedback control is well known as a practical method for stabilizing unstable periodic orbits embedded in chaotic attractors. The method is based on applying feedback perturbation proportional to the deviation of the current state of the system from its state one period in the past, so that the feedback signal vanishes when the stabilization of the target orbit is attained. Presented is the experimental implementation of the time- delayed feedback control to stabilize cardiac arrhythmias during VF. Second feedback control method is based on a proportional control where the feedback signal depends only on the present state of the system. In both control methods stabilization is achieved by forcing the dynamical system back to “maintain” the correct orbit by administering a defibrillation shock as an electrical current. In the first method, the control signal stabilizes the period of the chaotic orbit during VF, while the second control method terminates VF by forcing the system back into phase space orbits during sinus rhythm. Feedback signals are obtained in real time with the optical electrocardiogram and processed with the feedback controller which drives the custom made voltage-to-current converter that is able to produce arbitrary waveforms. The experimental results showed that proposed continuous feedback control methods can stabilize VF converting it into monomorphic tachycardia and sinus rhythm by administering low energy shocks.



Tung Le, Kim’s Lab

The bending energetics of double stranded DNA (dsDNA) at short length scales remains controversial. Notably, recent single-molecule experiments on DNA looping in the absence of proteins suggest that the wormlike chain (WLC) model fails to predict the looping probability of dsDNA shorter than its persistence length. However, measurement of the looping probability of short dsDNA is subject to significant statistical error because looping events are extremely rare in physiological salt conditions, and comparison to the WLC model is ambiguous because of the unknown geometry requirement for loop stabilization. In this work, we used a novel unlooping assay to investigate energetics of small DNA loops in physiological salt conditions. Based on the measured loop breakage rate vs. loop length, we find that the free energy stored in DNA loops can be well described by the WLC model down to 60 bp. We also observe strong signs of structural transitions below 60 bp, reminiscent of kink formation.